-
1
-
-
0025294114
-
Conformational sampling using high temperature molecular dynamics
-
Bruccoleri, R.E., Karplus, M.: Conformational sampling using high temperature molecular dynamics. Biopolymers 29, 1847-1862 (1990)
-
(1990)
Biopolymers
, vol.29
, pp. 1847-1862
-
-
Bruccoleri, R.E.1
Karplus, M.2
-
2
-
-
0037406075
-
Cyclic coordinate descent: A robotics algorithm for protein loop closure
-
Canutescu, A., Dunbrack Jr., R.: Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Sci. 12, 963-972 (2003)
-
(2003)
Protein Sci
, vol.12
, pp. 963-972
-
-
Canutescu, A.1
Dunbrack Jr., R.2
-
3
-
-
0042511005
-
A graph theory algorithm for protein side-chain prediction
-
Canutescu, A., Shelenkov, A., Dunbrack Jr., R.: A graph theory algorithm for protein side-chain prediction. Protein Sci. 12, 2001-2014 (2003)
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.1
Shelenkov, A.2
Dunbrack Jr., R.3
-
4
-
-
0033722428
-
Operational space dynamics: Efficient algorithm for modeling and control of branching mechanisms
-
San Francisco, CA, pp, IEEE Computer Society Press, Los Alamitos
-
Chang, K.S., Khatib, O.: Operational space dynamics: Efficient algorithm for modeling and control of branching mechanisms. In: Proc. IEEE Int. Conf. on Robotics and Automation, San Francisco, CA, pp. 850-856. IEEE Computer Society Press, Los Alamitos (2000)
-
(2000)
Proc. IEEE Int. Conf. on Robotics and Automation
, pp. 850-856
-
-
Chang, K.S.1
Khatib, O.2
-
5
-
-
2342557155
-
Geometric algorithms for the conformational analysis of long protein loops
-
Cortes, J., Simeon, T., Renaud-Simeon, M., Tran, V.: Geometric algorithms for the conformational analysis of long protein loops. J. Comp. Chem. 25, 956-967 (2004)
-
(2004)
J. Comp. Chem
, vol.25
, pp. 956-967
-
-
Cortes, J.1
Simeon, T.2
Renaud-Simeon, M.3
Tran, V.4
-
6
-
-
1442281405
-
A kinematic view of loop closure
-
Coutsias, E.A., Soek, C., Jacobson, M.P., Dill, K.A.: A kinematic view of loop closure. J. Comp. Chem. 25, 510-528 (2004)
-
(2004)
J. Comp. Chem
, vol.25
, pp. 510-528
-
-
Coutsias, E.A.1
Soek, C.2
Jacobson, M.P.3
Dill, K.A.4
-
7
-
-
0034237227
-
-
Deane, C.M., Blundell, T.L.: A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins: Struc., Func., and Gene. 40, 135-144 (2000)
-
Deane, C.M., Blundell, T.L.: A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins. Proteins: Struc., Func., and Gene. 40, 135-144 (2000)
-
-
-
-
8
-
-
0037375742
-
-
DePristo, M.A., de Bakker, P.I.W., Lovell, S.C., Blundell, T.L.: Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins: Struc., Func., and Gene. 51, 41-55 (2003)
-
DePristo, M.A., de Bakker, P.I.W., Lovell, S.C., Blundell, T.L.: Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins: Struc., Func., and Gene. 51, 41-55 (2003)
-
-
-
-
9
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A., Do, R.K.G., Sali, A.: Modeling of loops in protein structures. Protein Sci. 9, 1753-1773 (2000)
-
(2000)
Protein Sci
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.G.2
Sali, A.3
-
10
-
-
0004236492
-
-
3rd edn. John Hopkins University Press, Baltimore, MD
-
Golub, G., van Loan, C.: Matrix Computations, 3rd edn. John Hopkins University Press, Baltimore, MD (1996)
-
(1996)
Matrix Computations
-
-
Golub, G.1
van Loan, C.2
-
11
-
-
0002274891
-
Spheres, molecules and hidden surface removal
-
Halperin, D., Overmars, M.H.: Spheres, molecules and hidden surface removal. Comp. Geom. Theory and App. 11, 83-102 (1998)
-
(1998)
Comp. Geom. Theory and App
, vol.11
, pp. 83-102
-
-
Halperin, D.1
Overmars, M.H.2
-
12
-
-
1842532008
-
-
Jacobson, M.P., Pincus, D.L., Rapp, C.S., Day, T.J.F., Honig, B., Shaw, D.E., Friesner, R.A.: A hierarchical approach to all-atom protein loop prediction. Proteins: Struc., Func., and Bioinf. 55, 351-367 (2004)
-
Jacobson, M.P., Pincus, D.L., Rapp, C.S., Day, T.J.F., Honig, B., Shaw, D.E., Friesner, R.A.: A hierarchical approach to all-atom protein loop prediction. Proteins: Struc., Func., and Bioinf. 55, 351-367 (2004)
-
-
-
-
13
-
-
13444304144
-
Inverse kinematics in biology: The protein loop closure problem
-
Kolodny, R., Guibas, L., Levitt, M., Koehl, P.: Inverse kinematics in biology: the protein loop closure problem. Int. J. Robotics Research 24, 151-163 (2005)
-
(2005)
Int. J. Robotics Research
, vol.24
, pp. 151-163
-
-
Kolodny, R.1
Guibas, L.2
Levitt, M.3
Koehl, P.4
-
14
-
-
33747065536
-
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations
-
Okazaki, K., Koga, N., Takada, S., Onuchic, J.N., Wolynes, P.G.: Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. PNAS 103, 11844-11849 (2006)
-
(2006)
PNAS
, vol.103
, pp. 11844-11849
-
-
Okazaki, K.1
Koga, N.2
Takada, S.3
Onuchic, J.N.4
Wolynes, P.G.5
-
15
-
-
0034565516
-
Beyond genomic fold assignment: Rational modeling of proteins in bilological systems
-
Sauder, J.M., Dunbrack Jr., R.: Beyond genomic fold assignment: rational modeling of proteins in bilological systems. J. Mol. Biol. 8, 296-306 (2000)
-
(2000)
J. Mol. Biol
, vol.8
, pp. 296-306
-
-
Sauder, J.M.1
Dunbrack Jr., R.2
-
16
-
-
33748281380
-
-
Shehu, A., Clementi, C., Kavraki, L.E.: Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations. Proteins: Struc., Func., and Bioinf. 65, 164-179 (2006)
-
Shehu, A., Clementi, C., Kavraki, L.E.: Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations. Proteins: Struc., Func., and Bioinf. 65, 164-179 (2006)
-
-
-
-
17
-
-
33748276474
-
-
Sousa, S.F., Fernandes, P.A., Ramos, M.J.: Protein-ligand docking: Current status and future challenges. Proteins: Struc., Func., and Bioinf. 65, 15-26 (2006)
-
Sousa, S.F., Fernandes, P.A., Ramos, M.J.: Protein-ligand docking: Current status and future challenges. Proteins: Struc., Func., and Bioinf. 65, 15-26 (2006)
-
-
-
-
18
-
-
0036096608
-
A divide and conquer approach to fast loop modeling
-
Tossato, C.E., Bindewald, E., Hesser, J., Manner, R.: A divide and conquer approach to fast loop modeling. Protein Eng. 15, 279-286 (2002)
-
(2002)
Protein Eng
, vol.15
, pp. 279-286
-
-
Tossato, C.E.1
Bindewald, E.2
Hesser, J.3
Manner, R.4
-
19
-
-
21644476812
-
Real-space protein-model completion: An inverse-kinematic approach
-
van den Bedem, H., Lotan, I., Latombe, J.C., Deacon, A.: Real-space protein-model completion: an inverse-kinematic approach, Acta Cryst. D61, 2-13 (2005)
-
(2005)
Acta Cryst
, vol.D61
, pp. 2-13
-
-
van den Bedem, H.1
Lotan, I.2
Latombe, J.C.3
Deacon, A.4
-
20
-
-
0031564640
-
PDB-based protein loop prediction: Parameters for selection and methods for optimization
-
van Vlijmen, H.W.T., Karplus, M.: PDB-based protein loop prediction: parameters for selection and methods for optimization. J. Mol. Biol. 267, 975-1001 (1997)
-
(1997)
J. Mol. Biol
, vol.267
, pp. 975-1001
-
-
van Vlijmen, H.W.T.1
Karplus, M.2
-
21
-
-
0000781576
-
Exact analytical loop closure in proteins using polynomial equations
-
Wedemeyer, W.J., Scheraga, H.A.: Exact analytical loop closure in proteins using polynomial equations. J. Comp. Chem. 20, 819-844 (1999)
-
(1999)
J. Comp. Chem
, vol.20
, pp. 819-844
-
-
Wedemeyer, W.J.1
Scheraga, H.A.2
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